Robust information of genetic diversity among Bt cotton genotypes is still lacking and availability of several marker systems has prompted us to compare their utility for the detection of genetic diversity. Here, we report the comparative efficiency of morphological and molecular markers (EST-SSRs and ISSRs) in determining the genetic diversity among 30 Pakistani Bt cotton genotypes. Three different dendrograms based on 20 EST-SSRs, 13 ISSRs and 20 morphological markers divided the 30 Bt cotton genotypes into five, six, and three clusters, respectively. EST-SSRs and ISSRs revealed 0.73-1.00 and 0.77-0.97 genetics similarity among Bt cotton genotypes which indicated low level of genetic diversity. Further population structure analysis showed extensive allelic admixture among Bt cotton cultivars and identified three (EST-SSRs) and six (ISSRs) subgroups. The MGHES-31 (EST-SSRs) and UBC-807 and UBC-815 (ISSRs) showed maximum values of Polymorphic Information Contents(PIC) and Dj and had low value of Cj. The comparison of two marker systems showed that EST-SSRs had high value of Expected heterozygosity (H_ep) and low value of Marker Index (MI) as compared to ISSRs. In conclusion, high level of genetic similarity among Bt cotton genotypes compel the plant breeders for the introduction of divers/exotic genotypes in their breeding program and marker discriminating indices could be a potential tool for selection of particular marker system to unveil the genetic difference.

Keywords: Confusion probability, Expected heterozygosity, Marker Index, Population structure analysis, Polymorphic information contents

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